The functions that define XH:
dXHdt– compute derivativesUpdate_XHt– update state variablesF_H– compute host population densityF_I– compute infectious host population sizeF_infectivity– compute infectivity (pre-erythrocytic immunity)F_ni– compute net infectiousnessF_prevalence– compute true prevalenceF_pfpr_by_lm– compute prevalence by light microscopyF_pfpr_by_rdt– compute prevalence by RDTF_pfpr_by_pcr– compute prevalence by PCRget_HTC– compute human transmitting capacitysetup_XH_obj– set up the XH module objectsetup_XH_ix– set index valuessetup_XH_inits– set up initial valuesget_XH_inits– get initial valueschange_XH_inits– change initial valuesget_XH_vars– list state variablesget_XH_ix– get variable indicesget_XH_pars– get parameterschange_XH_pars– change parameterschange_H– change host population densityparse_XH_orbits– parse outputsget_XH_orbits– get saved orbitsget_PR– get prevalence from orbitssteady_state_X– compute X steady state given FoI and Hsteady_state_XH– compute XH steady state given FoIxds_plot_X– plot X outputscheck_XH– run consistency checksskill_set_XH– return module skill set